Přehled o publikaci

A complex karyotype (CK) is among the negative prognostic markers in chronic lymphocytic leukemia (CLL). Modern high-throughput technologies, such as long-read sequencing (LRS), chromatin conformation analysis (Hi-C), and optical genome mapping (OGM), offer high-resolution genomic analysis. These methods may contribute to a better characterization of CK and an improved understanding of the molecular mechanisms driving disease progression and treatment response/resistance. Our aim was to evaluate the analytical potential of these methods in CK investigation. CK was determined using karyotyping methods and mFISH. High-molecular-weight DNA was sequenced on the PromethION platform (Oxford Nanopore Technologies); data were analyzed using the SVIM and Delly tools. For the analysis of structural variants (SVs) detected by OGM (Bionano Genomics), the Rare Variant Analysis approach was applied, while EagleC and NeoLoopFinder were used for detecting aberrations via the Hi-C method. We compared routine diagnostic methods with high-throughput techniques in 10 CLL patients with CK. Copy number variation (CNV) analysis produced consistent results across all methods. LRS and OGM were the most reliable for detecting deletions and duplications ≤20 kb. mFISH, OGM, and Hi-C effectively identified reciprocal translocations and simple derivative chromosomes. In contrast, LRS supported by mFISH enabled the detection of dicentric chromosomes and derivative chromosomes involving ≥3 chromosomes. LRS and OGM repeatedly demonstrated greater aberration complexity than traditional cytogenetic methods. Our results indicate that the most promising approach for CK resolution is a combination of advanced genomic analysis with standard methods. Each method has specific advantages and limitations. Moreover, new technologies contribute to a better understanding of the impact of SVs on the CLL phenotype.